tests/testthat/test_fileinput.R
In ipb-halle/MetFamily: MetFamily: Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies
test_that("trivial", {
expect_equal(1, 1)
})
test_that("exampledata", {
filePeakMatrix <- system.file("extdata/showcase/Metabolite_profile_showcase.txt", package = "MetFamily")
data <- parsePeakAbundanceMatrix(filePeakMatrix, doPrecursorDeisotoping=TRUE,
mzDeviationInPPM_precursorDeisotoping=10, mzDeviationAbsolute_precursorDeisotoping=0.01,
maximumRtDifference=0.05,
progress=FALSE)
## Test dimensions
expect_equal(nrow(data$dataFrame1), 5403)
expect_equal(ncol(data$dataFrame1), 20)
## Test some values
expect_true(all(summary(t(data$dataFrame1[1,c("TRI03", "TRI02", "TRI01", "LVS03", "LVS02", "LVS01")])) == c("Min. : 236.0 ", "1st Qu.: 306.2 ", "Median : 357.5 ", "Mean : 501.0 ", "3rd Qu.: 554.2 ", "Max. :1146.0 ")))
expect_true(all(round(summary(data$dataFrame1[, "TRI01"])) == c(0, 809, 1537, 9818, 3207, 4407926)))
})
test_that("MS-Dial 4.X", {
# filePeakMatrix <- system.file("extdata/showcase/Metabolite_profile_showcase.txt", package = "MetFamily")
# data <- parsePeakAbundanceMatrix(filePeakMatrix, doPrecursorDeisotoping,
# mzDeviationInPPM_precursorDeisotoping, mzDeviationAbsolute_precursorDeisotoping,
# maximumRtDifference,
# progress=FALSE)
#
# expect_equal(ncol(data$dataFrame), 41)
})
test_that("MSP reading works", {
if(FALSE) {
fileSpectra <- system.file("extdata/showcase/Metabolite_profile_showcase.msp", package = "MetFamily")
#load(system.file("extdata/testdata/readMSPreturnObj.Rdata", package = "MetFamily"))
returnObj <- parseMSP(fileSpectra = fileSpectra,
minimumIntensityOfMaximalMS2peak = 2000,
minimumProportionOfMS2peaks = 0.05,
neutralLossesPrecursorToFragments = TRUE,
neutralLossesFragmentsToFragments = FALSE,
progress = FALSE)
expect_equal(returnObj$numberOfSpectra, 2640)
expect_equal(returnObj$numberOfSpectraOriginal, 5824)
expect_equal(returnObj$numberOfMS2PeaksOriginal, 145973)
expect_equal(returnObj$numberOfMS2PeaksWithNeutralLosses, 68738)
expect_equal(returnObj$numberOfMS2PeaksAboveThreshold, 34369)
expect_equal(returnObj$numberOfMS2PeaksBelowThreshold, 109797)
expect_equal(returnObj$numberOfTooHeavyFragments, 1807)
expect_equal(returnObj$numberOfSpectraDiscardedDueToNoPeaks, 15)
expect_equal(returnObj$numberOfSpectraDiscardedDueToMaxIntensity, 3163)
expect_equal(returnObj$numberOfSpectraDiscardedDueToTooHeavy, 5)
expect_equal(length(returnObj$precursorMz), 2640)
expect_equal(returnObj$precursorMz[1], 85)
expect_equal(length(returnObj$precursorRt), 2640)
expect_equal(returnObj$precursorRt[1], 10.98)
}
# > str(returnObj, max.level = 1)
# List of 14
# $ fileSpectra : chr "/tmp/RtmpL82I4E/ff16bb92ac5e87cb202eec2e/0.msp"
# $ spectraList :List of 2640
# $ numberOfSpectra : int 2640
# $ numberOfSpectraOriginal : int 5824
# $ numberOfMS2PeaksOriginal : num 145973
# $ numberOfMS2PeaksWithNeutralLosses : num 68738
# $ numberOfMS2PeaksAboveThreshold : num 34369
# $ numberOfMS2PeaksBelowThreshold : num 109797
# $ numberOfTooHeavyFragments : num 1807
# $ numberOfSpectraDiscardedDueToNoPeaks : num 15
# $ numberOfSpectraDiscardedDueToMaxIntensity: num 3163
# $ numberOfSpectraDiscardedDueToTooHeavy : num 5
# $ precursorMz : num [1:2640] 85 85 85 85 85 ...
# $ precursorRt : num [1:2640] 10.98 7.42 12.4 16.26 13 ...
#
##
## returnObj contains the following elements:
##
# returnObj <- list()
# returnObj$fileSpectra <- fileSpectra
# returnObj$spectraList <- list()
# returnObj$numberOfSpectra <- 0
# returnObj$numberOfMS2PeaksOriginal <- 0
# returnObj$numberOfMS2PeaksWithNeutralLosses <- 0
# returnObj$numberOfMS2PeaksAboveThreshold <- 0
# returnObj$numberOfMS2PeaksBelowThreshold <- 0
# returnObj$precursorMz <- vector(mode = "numeric")
# returnObj$precursorRt <- vector(mode = "numeric")
})
test_that("Project reading works", {
fileName <- system.file("extdata/showcase/Project_file_showcase_annotated.csv.gz", package = "MetFamily")
readDataList <- readClusterDataFromProjectFile(
file = fileName,
progress = FALSE)
#load("inst/extdata/testdata/readClusterDataFromProjectFile.Rdata")
expect_equal(length(readDataList), 59)
expect_equal(nrow(readDataList$dataFrameHeader), 3)
expect_equal(ncol(readDataList$dataFrameHeader), 14570)
expect_equal(length(readDataList$importParameterSet), 19)
#
# > str(dataList, max.level = 1)
# List of 59
# $ dataFrameHeader :'data.frame': 3 obs. of 14570 variables:
# $ dataFrameMS1Header :'data.frame': 3 obs. of 23 variables:
# $ dataFrameInfos :'data.frame': 2585 obs. of 23 variables:
# $ importParameterSet :List of 19
# $ numberOfPrecursors : int 2585
# $ numberOfDuplicatedPrecursors : int 0
# $ grouXXXps : chr [1:2] "TRI" "LVS"
# $ columnGroupLabels : chr [1:3, 1:2] "TRI" "TRI" "TRI" "LVS" ...
# ..- attr(*, "dimnames")=List of 2
# $ groupSampleDataFrame :'data.frame': 6 obs. of 4 variables:
# $ metaboliteProfileColumnNames : chr [1:23] "m/z" "RT" "Annotation" "Alignment ID" ...
# $ tagsSector : chr [1:23] "ID" "ID" "AnnotationColors={AS=#0000FF, SQT-glucosides=#FF0000}" "" ...
# $ fragmentMasses : num [1:14547] 69 71 71 71 73 ...
# $ fragmentFrequency : int [1:14547] 19 149 3 4 15 77 1 6 11 1 ...
# $ fragmentAbundance : num [1:14547] 0.1162 0.0899 0.131 0.1033 0.1987 ...
# $ minimumMass : num -1008
# $ maximumMass : num 1198
# $ precursorLabels : chr [1:2585] " 85.005 / 7.42" " 85.005 / 10.98" " 85.005 / 8.58" " 85.005 / 12.40" ...
# $ dataFrameMeasurements :'data.frame': 2585 obs. of 13 variables:
# $ meanAllMax : num 2441679
# $ logFoldChangeMax : num 10.5
# $ logAbsMax : num 6.7
# $ colorMatrixDataFrame : chr [1:2585, 1:13] "#8AFF00" "#E0FF00" "#9CFF00" "#EBFF00" ...
# ..- attr(*, "dimnames")=List of 2
# $ colorMapAbsoluteData :List of 6
# $ colorMapLogFoldChange :List of 6
# $ dataColumnsNameFunctionFromGroupName :function (group, sampleNamesToExclude)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 666 43 668 3 43 3 3786 3788
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ dataColumnsNameFunctionFromGroupIndex :function (groupIdx, sampleNamesToExclude)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 662 44 664 3 44 3 3782 3784
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ dataColumnsNameFunctionFromGroupNames :function (grouXXXps, sampleNamesToExclude)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 670 44 674 3 44 3 3790 3794
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ groupNameFunctionFromDataColumnName :function (dataColumnName, sampleNamesToExclude)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 676 42 682 3 42 3 3796 3802
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ lfcColumnNameFunctionFromString :function (columnName)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 464 38 469 3 38 3 3584 3589
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ dataMeanColumnNameFunctionFromString :function (columnName)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 470 43 473 3 43 3 3590 3593
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ dataColumnIndecesFunctionFromGroupIndex:function (groupIdx, sampleNamesToExclude)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 658 46 660 3 46 3 3778 3780
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ dataMeanColumnNameFunctionFromName :function (group)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 800 42 802 3 42 3 3920 3922
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ dataMeanColumnNameFunctionFromIndex :function (groupIdx)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 804 43 806 3 43 3 3924 3926
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ lfcColumnNameFunctionFromName :function (groupOne, groupTwo)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 808 36 810 3 36 3 3928 3930
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ lfcColumnNameFunctionFromIndex :function (groupIdxOne, groupIdxTwo)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 812 37 814 3 37 3 3932 3934
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ groupNameFromGroupIndex :function (groupIdx)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 816 30 818 3 30 3 3936 3938
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ groupIdxFromGroupName :function (group)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 820 28 822 3 28 3 3940 3942
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ featureMatrix :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
# $ featureIndeces :List of 2585
# $ featureCount : num [1:2585] 1 1 1 1 1 1 1 1 1 1 ...
# $ featureIndexMatrix : int [1:2585, 1:90] 15 15 15 15 15 15 15 15 15 15 ...
# ..- attr(*, "dimnames")=List of 2
# $ ms2_numberOfFragments : int [1:14547] 19 149 3 4 15 77 1 6 11 1 ...
# $ ms2_averageAbundance : num [1:14547] 0.1162 0.0899 0.131 0.1033 0.1987 ...
# $ ms2_masses : num [1:14547] 69 71 71 71 73 ...
# $ colorMapFragmentData :List of 6
# $ annotationColumnName : chr "Annotation"
# $ annotationColorsName : chr "AnnotationColors"
# $ annotationColumnIndex : int 3
# $ annotationValueIgnore : chr "Ignore"
# $ annotationColorIgnore : chr "red"
# $ annoArrayOfLists :List of 2585
# $ annoArrayIsArtifact : logi [1:2585] FALSE FALSE FALSE FALSE FALSE FALSE ...
# $ annoPresentAnnotationsList :List of 3
# $ annoPresentColorsList :List of 3
# $ orderColumnNames :function (groupSampleDataFrame, columnNames)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 685 23 691 3 23 3 3805 3811
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ excludedSamples :function (groupSampleDataFrame, grouXXXps = dataList$grouXXXps)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 695 22 700 3 22 3 3815 3820
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ includedSamples :function (groupSampleDataFrame, grouXXXps = dataList$grouXXXps)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 702 22 707 3 22 3 3822 3827
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ includedGroups :function (groupSampleDataFrame, samples = dataList$groupSampleDataFrame[, "Sample"])
# ..- attr(*, "srcref")= 'srcref' int [1:8] 710 21 714 3 21 3 3830 3834
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ excludedGroups :function (groupSampleDataFrame, samples = dataList$groupSampleDataFrame[, "Sample"])
# ..- attr(*, "srcref")= 'srcref' int [1:8] 716 21 718 3 21 3 3836 3838
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
#
#
#
})
ipb-halle/MetFamily documentation built on Sept. 5, 2024, 12:01 a.m.
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test_that("trivial", {
expect_equal(1, 1)
})
test_that("exampledata", {
filePeakMatrix <- system.file("extdata/showcase/Metabolite_profile_showcase.txt", package = "MetFamily")
data <- parsePeakAbundanceMatrix(filePeakMatrix, doPrecursorDeisotoping=TRUE,
mzDeviationInPPM_precursorDeisotoping=10, mzDeviationAbsolute_precursorDeisotoping=0.01,
maximumRtDifference=0.05,
progress=FALSE)
## Test dimensions
expect_equal(nrow(data$dataFrame1), 5403)
expect_equal(ncol(data$dataFrame1), 20)
## Test some values
expect_true(all(summary(t(data$dataFrame1[1,c("TRI03", "TRI02", "TRI01", "LVS03", "LVS02", "LVS01")])) == c("Min. : 236.0 ", "1st Qu.: 306.2 ", "Median : 357.5 ", "Mean : 501.0 ", "3rd Qu.: 554.2 ", "Max. :1146.0 ")))
expect_true(all(round(summary(data$dataFrame1[, "TRI01"])) == c(0, 809, 1537, 9818, 3207, 4407926)))
})
test_that("MS-Dial 4.X", {
# filePeakMatrix <- system.file("extdata/showcase/Metabolite_profile_showcase.txt", package = "MetFamily")
# data <- parsePeakAbundanceMatrix(filePeakMatrix, doPrecursorDeisotoping,
# mzDeviationInPPM_precursorDeisotoping, mzDeviationAbsolute_precursorDeisotoping,
# maximumRtDifference,
# progress=FALSE)
#
# expect_equal(ncol(data$dataFrame), 41)
})
test_that("MSP reading works", {
if(FALSE) {
fileSpectra <- system.file("extdata/showcase/Metabolite_profile_showcase.msp", package = "MetFamily")
#load(system.file("extdata/testdata/readMSPreturnObj.Rdata", package = "MetFamily"))
returnObj <- parseMSP(fileSpectra = fileSpectra,
minimumIntensityOfMaximalMS2peak = 2000,
minimumProportionOfMS2peaks = 0.05,
neutralLossesPrecursorToFragments = TRUE,
neutralLossesFragmentsToFragments = FALSE,
progress = FALSE)
expect_equal(returnObj$numberOfSpectra, 2640)
expect_equal(returnObj$numberOfSpectraOriginal, 5824)
expect_equal(returnObj$numberOfMS2PeaksOriginal, 145973)
expect_equal(returnObj$numberOfMS2PeaksWithNeutralLosses, 68738)
expect_equal(returnObj$numberOfMS2PeaksAboveThreshold, 34369)
expect_equal(returnObj$numberOfMS2PeaksBelowThreshold, 109797)
expect_equal(returnObj$numberOfTooHeavyFragments, 1807)
expect_equal(returnObj$numberOfSpectraDiscardedDueToNoPeaks, 15)
expect_equal(returnObj$numberOfSpectraDiscardedDueToMaxIntensity, 3163)
expect_equal(returnObj$numberOfSpectraDiscardedDueToTooHeavy, 5)
expect_equal(length(returnObj$precursorMz), 2640)
expect_equal(returnObj$precursorMz[1], 85)
expect_equal(length(returnObj$precursorRt), 2640)
expect_equal(returnObj$precursorRt[1], 10.98)
}
# > str(returnObj, max.level = 1)
# List of 14
# $ fileSpectra : chr "/tmp/RtmpL82I4E/ff16bb92ac5e87cb202eec2e/0.msp"
# $ spectraList :List of 2640
# $ numberOfSpectra : int 2640
# $ numberOfSpectraOriginal : int 5824
# $ numberOfMS2PeaksOriginal : num 145973
# $ numberOfMS2PeaksWithNeutralLosses : num 68738
# $ numberOfMS2PeaksAboveThreshold : num 34369
# $ numberOfMS2PeaksBelowThreshold : num 109797
# $ numberOfTooHeavyFragments : num 1807
# $ numberOfSpectraDiscardedDueToNoPeaks : num 15
# $ numberOfSpectraDiscardedDueToMaxIntensity: num 3163
# $ numberOfSpectraDiscardedDueToTooHeavy : num 5
# $ precursorMz : num [1:2640] 85 85 85 85 85 ...
# $ precursorRt : num [1:2640] 10.98 7.42 12.4 16.26 13 ...
#
##
## returnObj contains the following elements:
##
# returnObj <- list()
# returnObj$fileSpectra <- fileSpectra
# returnObj$spectraList <- list()
# returnObj$numberOfSpectra <- 0
# returnObj$numberOfMS2PeaksOriginal <- 0
# returnObj$numberOfMS2PeaksWithNeutralLosses <- 0
# returnObj$numberOfMS2PeaksAboveThreshold <- 0
# returnObj$numberOfMS2PeaksBelowThreshold <- 0
# returnObj$precursorMz <- vector(mode = "numeric")
# returnObj$precursorRt <- vector(mode = "numeric")
})
test_that("Project reading works", {
fileName <- system.file("extdata/showcase/Project_file_showcase_annotated.csv.gz", package = "MetFamily")
readDataList <- readClusterDataFromProjectFile(
file = fileName,
progress = FALSE)
#load("inst/extdata/testdata/readClusterDataFromProjectFile.Rdata")
expect_equal(length(readDataList), 59)
expect_equal(nrow(readDataList$dataFrameHeader), 3)
expect_equal(ncol(readDataList$dataFrameHeader), 14570)
expect_equal(length(readDataList$importParameterSet), 19)
#
# > str(dataList, max.level = 1)
# List of 59
# $ dataFrameHeader :'data.frame': 3 obs. of 14570 variables:
# $ dataFrameMS1Header :'data.frame': 3 obs. of 23 variables:
# $ dataFrameInfos :'data.frame': 2585 obs. of 23 variables:
# $ importParameterSet :List of 19
# $ numberOfPrecursors : int 2585
# $ numberOfDuplicatedPrecursors : int 0
# $ grouXXXps : chr [1:2] "TRI" "LVS"
# $ columnGroupLabels : chr [1:3, 1:2] "TRI" "TRI" "TRI" "LVS" ...
# ..- attr(*, "dimnames")=List of 2
# $ groupSampleDataFrame :'data.frame': 6 obs. of 4 variables:
# $ metaboliteProfileColumnNames : chr [1:23] "m/z" "RT" "Annotation" "Alignment ID" ...
# $ tagsSector : chr [1:23] "ID" "ID" "AnnotationColors={AS=#0000FF, SQT-glucosides=#FF0000}" "" ...
# $ fragmentMasses : num [1:14547] 69 71 71 71 73 ...
# $ fragmentFrequency : int [1:14547] 19 149 3 4 15 77 1 6 11 1 ...
# $ fragmentAbundance : num [1:14547] 0.1162 0.0899 0.131 0.1033 0.1987 ...
# $ minimumMass : num -1008
# $ maximumMass : num 1198
# $ precursorLabels : chr [1:2585] " 85.005 / 7.42" " 85.005 / 10.98" " 85.005 / 8.58" " 85.005 / 12.40" ...
# $ dataFrameMeasurements :'data.frame': 2585 obs. of 13 variables:
# $ meanAllMax : num 2441679
# $ logFoldChangeMax : num 10.5
# $ logAbsMax : num 6.7
# $ colorMatrixDataFrame : chr [1:2585, 1:13] "#8AFF00" "#E0FF00" "#9CFF00" "#EBFF00" ...
# ..- attr(*, "dimnames")=List of 2
# $ colorMapAbsoluteData :List of 6
# $ colorMapLogFoldChange :List of 6
# $ dataColumnsNameFunctionFromGroupName :function (group, sampleNamesToExclude)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 666 43 668 3 43 3 3786 3788
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ dataColumnsNameFunctionFromGroupIndex :function (groupIdx, sampleNamesToExclude)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 662 44 664 3 44 3 3782 3784
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ dataColumnsNameFunctionFromGroupNames :function (grouXXXps, sampleNamesToExclude)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 670 44 674 3 44 3 3790 3794
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ groupNameFunctionFromDataColumnName :function (dataColumnName, sampleNamesToExclude)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 676 42 682 3 42 3 3796 3802
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ lfcColumnNameFunctionFromString :function (columnName)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 464 38 469 3 38 3 3584 3589
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ dataMeanColumnNameFunctionFromString :function (columnName)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 470 43 473 3 43 3 3590 3593
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ dataColumnIndecesFunctionFromGroupIndex:function (groupIdx, sampleNamesToExclude)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 658 46 660 3 46 3 3778 3780
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ dataMeanColumnNameFunctionFromName :function (group)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 800 42 802 3 42 3 3920 3922
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ dataMeanColumnNameFunctionFromIndex :function (groupIdx)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 804 43 806 3 43 3 3924 3926
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ lfcColumnNameFunctionFromName :function (groupOne, groupTwo)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 808 36 810 3 36 3 3928 3930
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ lfcColumnNameFunctionFromIndex :function (groupIdxOne, groupIdxTwo)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 812 37 814 3 37 3 3932 3934
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ groupNameFromGroupIndex :function (groupIdx)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 816 30 818 3 30 3 3936 3938
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ groupIdxFromGroupName :function (group)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 820 28 822 3 28 3 3940 3942
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ featureMatrix :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
# $ featureIndeces :List of 2585
# $ featureCount : num [1:2585] 1 1 1 1 1 1 1 1 1 1 ...
# $ featureIndexMatrix : int [1:2585, 1:90] 15 15 15 15 15 15 15 15 15 15 ...
# ..- attr(*, "dimnames")=List of 2
# $ ms2_numberOfFragments : int [1:14547] 19 149 3 4 15 77 1 6 11 1 ...
# $ ms2_averageAbundance : num [1:14547] 0.1162 0.0899 0.131 0.1033 0.1987 ...
# $ ms2_masses : num [1:14547] 69 71 71 71 73 ...
# $ colorMapFragmentData :List of 6
# $ annotationColumnName : chr "Annotation"
# $ annotationColorsName : chr "AnnotationColors"
# $ annotationColumnIndex : int 3
# $ annotationValueIgnore : chr "Ignore"
# $ annotationColorIgnore : chr "red"
# $ annoArrayOfLists :List of 2585
# $ annoArrayIsArtifact : logi [1:2585] FALSE FALSE FALSE FALSE FALSE FALSE ...
# $ annoPresentAnnotationsList :List of 3
# $ annoPresentColorsList :List of 3
# $ orderColumnNames :function (groupSampleDataFrame, columnNames)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 685 23 691 3 23 3 3805 3811
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ excludedSamples :function (groupSampleDataFrame, grouXXXps = dataList$grouXXXps)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 695 22 700 3 22 3 3815 3820
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ includedSamples :function (groupSampleDataFrame, grouXXXps = dataList$grouXXXps)
# ..- attr(*, "srcref")= 'srcref' int [1:8] 702 22 707 3 22 3 3822 3827
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ includedGroups :function (groupSampleDataFrame, samples = dataList$groupSampleDataFrame[, "Sample"])
# ..- attr(*, "srcref")= 'srcref' int [1:8] 710 21 714 3 21 3 3830 3834
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
# $ excludedGroups :function (groupSampleDataFrame, samples = dataList$groupSampleDataFrame[, "Sample"])
# ..- attr(*, "srcref")= 'srcref' int [1:8] 716 21 718 3 21 3 3836 3838
# .. ..- attr(*, "srcfile")=Classes 'srcfilealias', 'srcfile' <environment: 0x555c0c5c55d0>
#
#
#
})
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